Geometric and potential driving formation and evolution of biomolecular surfaces
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Publication:843299
DOI10.1007/S00285-008-0226-7zbMATH Open1311.92212OpenAlexW2145645041WikidataQ51866051 ScholiaQ51866051MaRDI QIDQ843299FDOQ843299
Authors: Zhan Chen, Yuhui Sun, G. W. Wei, Shan Zhao, Peter W. Bates 
Publication date: 12 October 2009
Published in: Journal of Mathematical Biology (Search for Journal in Brave)
Full work available at URL: https://doi.org/10.1007/s00285-008-0226-7
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Biochemistry, molecular biology (92C40) Optimization of shapes other than minimal surfaces (49Q10) Minimal surfaces in differential geometry, surfaces with prescribed mean curvature (53A10) Finite difference methods for initial value and initial-boundary value problems involving PDEs (65M06) Molecular structure (graph-theoretic methods, methods of differential topology, etc.) (92E10) Classical flows, reactions, etc. in chemistry (92E20)
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Cited In (34)
- Explicit-solute implicit-solvent molecular simulation with binary level-set, adaptive-mobility, and GPU
- A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states
- Object-oriented persistent homology
- Biomolecular surface construction by PDE transform
- Quantum dynamics in continuum for proton transport. II: Variational solvent-solute interface
- A matched Peaceman-Rachford ADI method for solving parabolic interface problems
- Partial differential equation transform -- variational formulation and Fourier analysis
- Pseudo-time-coupled nonlinear models for biomolecular surface representation and solvation analysis
- Operator splitting ADI schemes for pseudo-time coupled nonlinear solvation simulations
- Stability of a Cylindrical Solute-Solvent Interface: Effect of Geometry, Electrostatics, and Hydrodynamics
- On developing stable finite element methods for pseudo-time simulation of biomolecular electrostatics
- Multiscale models of compact bone
- The mass-preserving solution-flux scheme for multi-layer interface parabolic equations
- High-order fractional partial differential equation transform for molecular surface construction
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- A topological approach for protein classification
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- Minimization and Eulerian formulation of differential geometry based nonpolar multiscale solvation models
- Differential geometry based solvation model II: Lagrangian formulation
- Differential geometry based multiscale models
- Dynamic maintenance of molecular surfaces under conformational changes
- Multiscale geometric modeling of macromolecules. I: Cartesian representation
- A regularization approach for solving the super-Gaussian Poisson-Boltzmann model with heterogeneous dielectric functions
- Convergence of a diffuse interface Poisson-Boltzmann (PB) model to the sharp interface PB model: a unified regularization formulation
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- A matched alternating direction implicit (ADI) method for solving the heat equation with interfaces
- Mode decomposition evolution equations
- A unified discontinuous Galerkin framework for time integration
- Multiscale molecular dynamics using the matched interface and boundary method
- On regularization of charge singularities in solving the Poisson-Boltzmann equation with a smooth solute-solvent boundary
- A new approach to constrained total variation solvation models and the study of solute-solvent interface profiles
- Fully implicit ADI schemes for solving the nonlinear Poisson-Boltzmann equation
- Numerical methods for solvent Stokes flow and solute-solvent interfacial dynamics of charged molecules
- Calculation of electrostatic free energy for the nonlinear Poisson-Boltzmann model based on the dimensionless potential
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